To do so, CHANGE-seq-BE starts with a whole genome, but instead of immediately sequencing it, scientists split the genome into tiny circles of DNA. They then take those circles and expose them to the base editor being tested. Afterward, they treat the DNA with a special enzyme that detects if base editing occurred, opening those — and only those — DNA circles with evidence of base editing into linear strands. The linear strands of DNA are then selectively sequenced, requiring far fewer resources than competing techniques. They optimized it for both major types of base editors (adenine and cytosine base editors). After developing the method, the scientists wanted to know if it truly was both more comprehensive and resource-efficient than conventional approaches, so they tested them head-to-head.
“When we directly compared it to other methods, CHANGE-seq-BE found almost all sites nominated by those methods, as well as many that it was exclusively able to detect,” Tsai said. “We showed that this unbiased approach was more sensitive while using only about 5% of the sequencing reads.”
Given the technique’s sensitivity, ease of use and efficient resource utilization, others have already begun adopting it. Full experimental protocols and software to enable CHANGE-seq-BE are described in the study, enabling this adoption. For example, in addition to the clinical application reported in the paper, clinical trials at St. Jude and beyond have integrated the technique into their planning, using it as a safety and efficiency evaluation tool. CHANGE-seq-BE was also recently used to characterize the first patient-specific in vivo genome editing treatment. Fundamental research labs investigating base editing have also begun using it to test for off-targets early in their process, better identifying the most promising approaches to pursue than existing screens. These early adopters show the technique’s appeal to researchers and clinicians alike, and its promise to push forward the future of base editing.
“We’ve enabled those developing these therapies to quickly understand and find the base editors with the highest potential activity and specificity,” Tsai said. “We hope that methods like CHANGE-seq-BE will open the door toward more genome editing therapies being developed for and reaching the patients who need them.”
Authors and funding
The study’s co-first authors are Cicera Lazzarotto, formerly of St. Jude; and Varun Katta, St. Jude. The study’s other authors are Yichao Li, Garret Manquen, Rachael Wood, Jacqueline Chyr and Azusa Matsubara, St. Jude; Elizabeth Urbina and GaHyun Lee, formerly of St. Jude; Xiaolin Wu, Frederick National Laboratory of Cancer Research; and Suk See De Ravin, National Institutes of Health.
The study was supported by grants from the National Institutes of Health Somatic Cell Genome Editing Consortium Program through National Institutes of Allergy and Infectious Diseases (U01AI176470 and U01AI176471), National Heart Lung and Blood Institute (U01HL163983), St. Jude Collaborative Research Consortium on Novel Gene Therapies for Sickle Cell Disease, St. Jude PARADIGM Blue Sky Project, the Doris Duke Charitable Foundation (2020154) and the American Lebanese Syrian Associated Charities (ALSAC), the fundraising and awareness organization of St. Jude.